Mots-Clés

cancer genomics, pipelines, GATK, python, snakemake

Description

Engineer position in bioinformatics or computational biology

Gustave Roussy

Position and Project title:

Processing of the cancer genomic and transcriptomic data

Research environment and project

Gustave Roussy, the premier European Cancer Centre, recruits an engineer in bioinformatics or computational biology to work on the joint project of Gustave Roussy, Université Paris-Saclay and other education/research institutions that aims at modeling cancer using integrative patient data for the development of novel precision medicine therapies.

An engineer position in bioinformatics is open in the laboratory of Cancer genomics (headed by Dr Sergey Nikolaev) in the Unit U981 INSERM, Gustave Roussy Cancer Center.

The project is dedicated to the study of damage induced mutagenesis in skin cancer and in other cancer types.

Our laboratory has generated a unique whole genome sequence dataset (DNA) for hundreds of skin tumors. Unique data generated in the lab include genomic sequencing of (i) the cohort of patients with Xeroderma pigmentosum (XP), which are characterized by up to 1’000 fold increased cancer risk (ii) the large cohort of non-melanoma skin cancers (iii) in-vitro and in-vivo knock-out models of XP. We leverage those data to understand genetic mechanisms of mutagenesis in the context of hypermutation and DNA repair deficiencies. For validation of the results we take advantage of public datasets, such as TCGA, ICGC, HARTWIG. 

Tasks:

The mission of an engineer will be to perform initial steps of genomic analyses: process sequencing files, do quality control, generate the lists of mutations and copy number alterations, produce representative graphs.

Develop components for cancer NGS data analysis, focusing on genomic / genomic DNA and RNA applications

• Develop and implement tools for accurate somatic variant detection from DNA sequencing
• Update the pipelines and genomic databases
• Implement tools for mutational signature analysis, copy number alterations and structural variant detection

 Qualifications:

• Experience with standard genomics software: BWA, GATK, SAMTools is required
• Experience with genomic analysis of NGS based DNA or RNA assays is required
• Experience developing bioinformatics pipelines and tools for NGS is required
• Advanced degree (PhD) in bioinformatics, genomics, or a related field is a plus
• Experience in cancer genomics is a plus
• Experience with cancer genomics software: Mutect2 etc. is a plus
• Experience of cancer variant detection – mutations, fusions, CNAs, (FACETS, MANTIS, etc)
• Familiarity with cancer databases: Cosmic, TCGA, PCAWG, HARTWIG.

Qualifications : 

Bioinformatics, computational biology, data science, biostatistics.  

Contract type:

Initial fixed-term 24-month contract, with possible extension. Salary dependents on experience. 

For queries about this position, please contact: Sergey.Nikolaev@gustaveroussy.fr